SMTL ID : 6oda.3 (2 other biounits)

Crystal structure of HDAC8 in complex with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

monomer

Ligands

1 x C7: N-{2-[3-(hydroxyamino)-3-oxopropyl]phenyl}-3-(trifluoromethyl)benzamide(Non-covalent)

C7.1: 11 residues within 4Å: Chain A: H.166, H.167, G.175, D.202, H.204, F.232, D.291, P.297, M.298, Y.330 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.232, A:P.297, A:Y.330 Hydrogen bonds: A:G.328 pi-Stacking: A:Y.330

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.202, H.204, D.291 Ligands: C7.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.202, A:D.202, A:H.204, A:D.291

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: F.213, T.216, V.219, Y.249, S.250 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:F.213, A:V.219 K.4: 6 residues within 4Å: Chain A: D.200, D.202, H.204, S.223, L.224, H.225 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.200, A:D.200, A:D.202, A:H.204, A:L.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Structure-based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-oxoimidazolidin-1-yl)phenyl)acrylamides as Potent and Selective HDAC8 inhibitors. To Be Published

Release Date

2020-04-01

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 8

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